- SCRIPTS and TOOLS for and INFORMATION on Running and Analysing Molecular Dynamics Simulations -
Short summary
This document should provide the reader with detailed information on starting and analysing molecular dynamics simulations with GROMACS. It is a collection of scripts and experiences made in our group. The focus lies on ionic liquids in bulk and slab geometry.
On the performance of parallelized Gromacs simulations of spatial inhomogeneous system (Slab geometry): domain decomposition and PME nodes
Short summary
We performed molecular dynamics (MD) simulations with Gromacs 4.5.5 to investigate the structural orientation of imidazole based room temperature ionic liquids (RTILs) at charged electrodes. The resulting configurations consist of 45000 to 50000 atoms per simulation box.
The amount of particles requires high parallelization, which requires some additional considerations due to the large unoccupied volume resulting in high spatial inhomogeneity. Some considerations for domain decomposition and node partitioning are given in this document.
Result: When assigning number of PME nodes and domain decomposition by hand it is possible to increase the performace by 5-10 %. More over it is possible to increase the total number of nodes used for a simulation and thus increase the total performance by 50-100 % compared to the maximum number of nodes Gromacs is automatically able to use.
Computational Physical Chemistry
- SCRIPTS and TOOLS for and INFORMATION on Running and Analysing Molecular Dynamics Simulations -
Short summary
This document should provide the reader with detailed information on starting and analysing molecular dynamics simulations with GROMACS. It is a collection of scripts and experiences made in our group. The focus lies on ionic liquids in bulk and slab geometry.
On the performance of parallelized Gromacs simulations of spatial inhomogeneous system (Slab geometry): domain decomposition and PME nodes
Short summary
We performed molecular dynamics (MD) simulations with Gromacs 4.5.5 to investigate the structural orientation of imidazole based room temperature ionic liquids (RTILs) at charged electrodes. The resulting configurations consist of 45000 to 50000 atoms per simulation box.
The amount of particles requires high parallelization, which requires some additional considerations due to the large unoccupied volume resulting in high spatial inhomogeneity. Some considerations for domain decomposition and node partitioning are given in this document.
Result: When assigning number of PME nodes and domain decomposition by hand it is possible to increase the performace by 5-10 %. More over it is possible to increase the total number of nodes used for a simulation and thus increase the total performance by 50-100 % compared to the maximum number of nodes Gromacs is automatically able to use.